Developmental manifestations of polygenic risk for bipolar disorder from infancy to middle childhood

Knowledge on how genetic risk for bipolar disorder manifests in developmental, emotional or behavioral traits during childhood is lacking. This issue is important to address to inform early detection and intervention efforts. We investigated whether polygenic risk for bipolar disorder is associated with developmental outcomes during early to middle childhood in the general population, and if associations differ between boys and girls. Our sample consisted of 28 001 children from the Norwegian Mother, Father and Child Cohort study, a prospective pregnancy cohort with available genotype and developmental data. Mothers reported on a range of developmental outcomes in their children at 6 and 18 months, 3, 5 and 8 years. Polygenic risk scores reflecting common variant liability to bipolar disorder were calculated. Linear regression models were used in a multi-group framework to investigate associations between polygenic risk score and developmental outcomes, using sex as a grouping variable. We found robust evidence for an association between polygenic risk scores for bipolar disorder and conduct difficulties (β = 0.041, CI = 0.020–0.062) and oppositional defiant difficulties (β = 0.032, CI = 0.014–0.051) at 8 years. Associations with most other outcomes were estimated within the region of practical equivalence to zero (equivalence range D = −0.1 to 0.1), with the exceptions of negative association for activity levels (β = −0.028, CI = −0.047– −0.010) at age 5 and benevolence (β = −0.025, CI = –0.043 to –0.008) at age 8, and positive association for motor difficulties (β = 0.025, CI = 0.008–0.043) at age 3, inattention (β = 0.021, CI = 0.003–0.041) and hyperactivity (β = 0.025, CI = 0.006–0.044) at age 8. Our results suggest that genetic risk for bipolar disorder manifests as disruptive behaviors like oppositional defiant and conduct difficulties in childhood in the general population.


Supplementary Information content
years and 5 years we used the aggression subscale with statements like "Gets into many fights" and "Hits others". The CBCL also has an internalizing behavior measure, used for the Emotional difficulties measure in the study. Example of statements; "Clings to adults or too dependent", "Disturbed by any change in routine". These measures were available at 18 months, 3 years and 5 years.

Conners' Parent Rating Scale (CPRS-R):
The CPRS-R 8 is used for measuring hyperactivity and inattention at 5 years with statements like "short attention span" and "fidgets with hands or feet, squirms in seat".  Individuals were excluded if they had a genotyping call rate below 95% or autosomal heterozygosity greater than four standard deviations from the sample mean. SNPs were excluded if they were ambiguous (A / T and C / G), had a genotyping call rate below 98%, minor allele frequency of less than 1%, or Hardy-Weinberg equilibrium P-value less than 1 × 10-6. Population stratification was assessed, using the HapMap phase 3 release 3 as a reference, by principal component analysis using EIGENSTRAT version 6.1.4. Visual inspection identified a homogenous population of European ethnicity and individuals of non-European ethnicity were removed. Individuals with a genotyping call rate below 98% or autosomal heterozygosity greater than four standard deviations from the sample mean were then removed. A sex check was done by assessing the sex declared in the pedigree with the genetic sex, which was imputed based on the heterozygosity of chromosome X. When sex discrepancies were identified, the individual was flagged. Relatedness was assessed by flagging one individual from each pairwise comparison of identity-by-descent with a pi-hat greater than 0.1.
The parents and offspring datasets were then merged into one dataset per genotyping batch; keeping only the SNPs that passed quality control in both datasets. All individuals passing the genotyping call rate and autosomal heterozygosity measures were included in the merged datasets.
Therefore, the merged datasets included individuals previously excluded or flagged as a duplicate, ethnic outlier, having a sex discrepancy, or high level of relatedness. Concordance checks were then conducted on validated duplicates. Duplicate, tri-allelic and discordant (any discordance between the validated duplicates) SNPs were excluded. Individuals and SNPs with a genotyping call rate below 98% in the merged datasets were excluded. The duplicate sample that was removed before the start of the quality control was then excluded. Mendelian errors identified by the assessment of duos and trios were then recoded to missing. Insertions and deletions were also excluded.
Phasing was conducted using Shapeit 2 release 837 and the duoHMM approach was used to account for the pedigree structure. Imputation was conducted using IMPUTE4 and the publicly available Haplotype reference consortium (HRC) release 1-1 was used as the genetic reference panel. The Sanger Imputation Server was used to perform the imputation with the Positional Burrows-Wheeler Transform (PBWT). The phasing and imputation were conducted separately for each genotyping batch.
Post imputation quality control was performed by initially converting the dosages to best-guess genotypes. Individuals were removed if they had a genotyping call rate less than 99% or were of non-European ethnicity. SNPs with an imputation INFO quality score less than 0.8, genotyping call rate less than 98%, minor allele frequency less than 1%, or a Hardy-Weinberg equilibrium P-value less than 1 × 10-6 were removed. After quality control, a core homogeneous sample of European ethnicity (based on PCA of markers overlapping with available HapMap markers), unrelated (within generation, defined as accumulated identity-by-descent <0.015 and overall identity-by-descent PI_HAT <10%) individuals across all batches and arrays were available for use in analysis (Nchildren = 28,026).

Supplementary Figure 1. Correlation matrix of the dimensional measures
Note: The correlation matrix is in the order by age of the child when the parents answered the questionnaire.